rs12644393

Positions:

• chr4-117269425-G-A
• chr4-117269425-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.432 in 151,672 control chromosomes in the GnomAD database, including 14,604 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.43 (14604 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.844

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.551 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.432 AC: 65542 AN: 151554 Hom.: 14584 Cov.: 32

Gnomad AFR AF: 0.346

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.561

Gnomad ASJ AF: 0.460

Gnomad EAS AF: 0.259

Gnomad SAS AF: 0.456

Gnomad FIN AF: 0.494

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.477

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.432 AC: 65592 AN: 151672 Hom.: 14604 Cov.: 32 AF XY: 0.438 AC XY: 32478 AN XY: 74106

Gnomad4 AFR AF: 0.347

Gnomad4 AMR AF: 0.561

Gnomad4 ASJ AF: 0.460

Gnomad4 EAS AF: 0.259

Gnomad4 SAS AF: 0.456

Gnomad4 FIN AF: 0.494

Gnomad4 NFE AF: 0.457

Gnomad4 OTH AF: 0.477

Alfa AF: 0.459 Hom.: 20803

Bravo AF: 0.433

Asia WGS AF: 0.371 AC: 1291 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.15
DANN	Benign	0.56

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs12644393; hg19: chr4-118190581;